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updated un[aired stats with n_obs_complete and removed mediator vitd from sam and npa

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Tanushree Tunstall 2020-10-30 13:04:45 +00:00
parent 1b5d353060
commit a2dbecd03d
5 changed files with 165 additions and 65 deletions
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67
flu_stats_unpaired_serum.R
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@ -67,8 +67,8 @@ ci = which(is.na(lf_t1$value))
lf_t1_comp = lf_t1[-which(is.na(lf_t1$value)),]
stats_un_t1 = compare_means(value~obesity
, group.by = "mediator"
#, data = lf_t1
, data = lf_t1_comp
, data = lf_t1
#, data = lf_t1_comp
, paired = FALSE
, p.adjust.method = my_adjust_method)
@ -79,10 +79,20 @@ stats_un_t1$timepoint = "t1"
stats_un_t1 = as.data.frame(stats_un_t1)
class(stats_un_t1)
# calculate n_obs for each mediator
n_t1 = data.frame(table(lf_t1_comp$mediator))
colnames(n_t1) = c("mediator", "n_obs")
n_t1$mediator = as.character(n_t1$mediator)
#----------------------------------------
# calculate n_obs for each mediator: t1
#----------------------------------------
#n_t1 = data.frame(table(lf_t1_comp$mediator))
n_t1_all = data.frame(table(lf_t1$mediator))
colnames(n_t1_all) = c("mediator", "n_obs")
n_t1_all$mediator = as.character(n_t1_all$mediator)
n_t1_comp = data.frame(table(lf_t1_comp$mediator))
colnames(n_t1_comp) = c("mediator", "n_obs_complete")
n_t1_comp$mediator = as.character(n_t1_comp$mediator)
merge_cols = intersect(names(n_t1_all), names(n_t1_comp)); merge_cols
n_t1= merge(n_t1_all, n_t1_comp, by = merge_cols, all = T)
#==================================
# Merge: merge stats + n_obs df
@ -119,8 +129,8 @@ lf_t2_comp = lf_t2[-which(is.na(lf_t2$value)),]
stats_un_t2 = compare_means(value~obesity
, group.by = "mediator"
#, data = lf_t2
, data = lf_t2_comp
, data = lf_t2
#, data = lf_t2_comp
, paired = FALSE
, p.adjust.method = my_adjust_method)
# add timepoint and convert to df
@ -128,10 +138,20 @@ stats_un_t2$timepoint = "t2"
stats_un_t2 = as.data.frame(stats_un_t2)
class(stats_un_t2)
# calculate n_obs for each mediator
n_t2 = data.frame(table(lf_t2_comp$mediator))
colnames(n_t2) = c("mediator", "n_obs")
n_t2$mediator = as.character(n_t2$mediator)
#----------------------------------------
# calculate n_obs for each mediator: t2
#----------------------------------------
#n_t2 = data.frame(table(lf_t2_comp$mediator))
n_t2_all = data.frame(table(lf_t2$mediator))
colnames(n_t2_all) = c("mediator", "n_obs")
n_t2_all$mediator = as.character(n_t2_all$mediator)
n_t2_comp = data.frame(table(lf_t2_comp$mediator))
colnames(n_t2_comp) = c("mediator", "n_obs_complete")
n_t2_comp$mediator = as.character(n_t2_comp$mediator)
merge_cols = intersect(names(n_t2_all), names(n_t2_comp)); merge_cols
n_t2= merge(n_t2_all, n_t2_comp, by = merge_cols, all = T)
#==================================
# Merge: merge stats + n_obs df
@ -168,8 +188,8 @@ lf_t3_comp = lf_t3[-which(is.na(lf_t3$value)),]
stats_un_t3 = compare_means(value~obesity
, group.by = "mediator"
#, data = lf_t3
, data = lf_t3_comp
, data = lf_t3
#, data = lf_t3_comp
, paired = FALSE
, p.adjust.method = my_adjust_method)
@ -178,11 +198,20 @@ stats_un_t3$timepoint = "t3"
stats_un_t3 = as.data.frame(stats_un_t3)
class(stats_un_t3)
#----------------------------------------
# calculate n_obs for each mediator: t3
#----------------------------------------
#n_t3 = data.frame(table(lf_t3_comp$mediator))
n_t3_all = data.frame(table(lf_t3$mediator))
colnames(n_t3_all) = c("mediator", "n_obs")
n_t3_all$mediator = as.character(n_t3_all$mediator)
# calculate n_obs for each mediator
n_t3 = data.frame(table(lf_t3_comp$mediator))
colnames(n_t3) = c("mediator", "n_obs")
n_t3$mediator = as.character(n_t3$mediator)
n_t3_comp = data.frame(table(lf_t3_comp$mediator))
colnames(n_t3_comp) = c("mediator", "n_obs_complete")
n_t3_comp$mediator = as.character(n_t3_comp$mediator)
merge_cols = intersect(names(n_t3_all), names(n_t3_comp)); merge_cols
n_t3 = merge(n_t3_all, n_t3_comp, by = merge_cols, all = T)
#==================================
# Merge: merge stats + n_obs df
@ -289,6 +318,7 @@ my_col_order2 = c("mediator"
, "timepoint"
, "sample_type"
, "n_obs"
, "n_obs_complete"
, "group1"
, "group2"
, "method"
@ -318,6 +348,7 @@ colnames(combined_unpaired_stats_f) = c("mediator"
, "timepoint"
, "sample_type"
, "n_obs"
, "n_obs_complete"
, "group1"
, "group2"
, "method"